RNA-methyltransferase TrmA is a dual-specific enzyme responsible for<i>C<sup>5</sup>-</i>methylation of uridine in both tmRNA and tRNA

Ranaei-Siadat, Ehsan; Fabret, Céline; Seijo, Bili; Dardel, Frédéric; Grosjean, Henri; Nonin‐Lecomte, Sylvie

doi:10.4161/rna.24327

Cited by 29 publications

(26 citation statements)

References 25 publications

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“…Interestingly, some enzymes from the Trm10 family can methylate both adenosine and guanosine at position 9 of tRNAs . Multispecific enzymes that modify tRNAs as well as other RNA substrates include bacterial TrmA from E. coli that has been shown to also introduce m 5 U54 in tmRNA , bacterial RlmN from E. coli that catalyzes m 2 A modification both at position 2,503 of 23S rRNA and at position 37 of several tRNAs , and eukaryotic TRMT61B that catalyzes m 1 A formation both at position 58 of mitochondrial tRNAs and at position 947 of human mitochondrial 16S rRNA . Finally, it is worth mentioning that some RNA modifications found in mRNAs are likely introduced by tRNA modification enzymes .…”

Section: Determinants Of Specificity In Trna Modification Enzymesmentioning

confidence: 99%

To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs

Barraud

Tisné

2019

IUBMB Life

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Transfer RNAs (tRNAs) are essential components of the cellular protein synthesis machineries, but are also implicated in many roles outside translation. To become functional, tRNAs, initially transcribed as longer precursor tRNAs, undergo a tightly controlled biogenesis process comprising the maturation of their extremities, removal of intronic sequences if present, addition of the 3′‐CCA amino‐acid accepting sequence, and aminoacylation. In addition, the most impressive feature of tRNA biogenesis consists in the incorporation of a large number of posttranscriptional chemical modifications along its sequence. The chemical nature of these modifications is highly diverse, with more than hundred different modifications identified in tRNAs to date. All functions of tRNAs in cells are controlled and modulated by modifications, making the understanding of the mechanisms that determine and influence nucleotide modifications in tRNAs an essential point in tRNA biology. This review describes the different aspects that determine whether a certain position in a tRNA molecule is modified or not. We describe how sequence and structural determinants, as well as the presence of prior modifications control modification processes. We also describe how environmental factors and cellular stresses influence the level and/or the nature of certain modifications introduced in tRNAs, and report situations where these dynamic modulations of tRNA modification levels are regulated by active demodification processes. © 2019 IUBMB Life, 71(8):1126–1140, 2019

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Section: Determinants Of Specificity In Trna Modification Enzymesmentioning

confidence: 99%

To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs

Barraud

Tisné

2019

IUBMB Life

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“…The SAM-dependent pathway is the most common and uses a mechanism similar to 5methylcytosine DNA and RNA methyltransferases. In most characterized organisms, m 5 U54 in tRNAs and at the corresponding position in bacterial tmRNA is synthesized by a SAM-dependent methyltransferase, such as the Escherichia coli enzyme TrmA [31][32][33]. In addition, m 5 U1939 that is present in most bacterial 23S rRNAs, and m 5 U747 which is less common and found mainly in Gramnegative Beta, Epsilon and Gamma Proteobacteria, are respectively catalyzed by the SAM-dependent RlmD (formerly RumA) and RlmC (formerly RumB) methyltransferases [34,35].…”

Section: Of 20mentioning

confidence: 99%

Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes

Sirand‐Pugnet¹,

Brégeon²,

Béven³

et al. 2020

Preprint

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The C5-methylation of uracil to form 5-methyluracil (m 5 U) is a ubiquitous base modification of nucleic acids. Four enzyme families have converged to catalyze this methylation using different chemical solutions. Here, we investigate the evolution of 5-methyluracil synthase families in Mollicutes, a class of bacteria that has undergone extensive genome erosion. Many mollicutes have lost some of the m 5 U methyltransferases present in their common ancestor. Cases of duplication and subsequent shift of function are also described. For example, most members of the Spiroplasma subgroup, use the ancestral tetrahydrofolate-dependent TrmFO enzyme, to catalyze the formation of m 5 U54 in tRNA, while a TrmFO paralog (termed RlmFO) is responsible for m 5 U1939 formation in 23S RNA. RlmFO has replaced the S-adenosyl-l-methionine (SAM)enzyme RlmD that adds the same modification in the ancestor and which is still present in mollicutes from the Hominis subgroup. Another paralog of this family, the TrmFO-like protein, has a yet unidentified function that differs from the TrmFO and RlmFO homologs. Despite having evolved towards minimal genomes, the mollicutes possess a repertoire of m 5 U modifying enzymes that is highly dynamic and has undergone horizontal transfer. This emphasizes the necessity for combining bioinformatics predictions with empirical testing and structural information to get a reliable functional annotation of these enzymes.

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“…The tRNA-like structure includes a canonical T-stem-loop but a reduced D-loop devoid of a stem. It also contains the two modified nucleosides, 5-methyluridine and pseudouridine within the T loop, but not the dihydrouridine that usually is present in tRNAs [39,40]. Specific interactions between the D-and T-loops are necessary for the binding and functioning of SmpB [41], while the T-stem and acceptor stem bind the elongation factor-thermounstable (EF-Tu).…”

Section: Trna-like Domainmentioning

confidence: 99%

Bacterialtrans-Translation: From Functions to Applications

Giudice

Gillet

2014

Encyclopedia of Molecular Cell Biology and Molecular Medicine

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RNA-methyltransferase TrmA is a dual-specific enzyme responsible forC⁵-methylation of uridine in both tmRNA and tRNA

Cited by 29 publications

References 25 publications

To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs

To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs

Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes

Bacterialtrans-Translation: From Functions to Applications

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RNA-methyltransferase TrmA is a dual-specific enzyme responsible forC5-methylation of uridine in both tmRNA and tRNA

Cited by 29 publications

References 25 publications

To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs

To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs

Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes

Bacterialtrans-Translation: From Functions to Applications

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RNA-methyltransferase TrmA is a dual-specific enzyme responsible forC⁵-methylation of uridine in both tmRNA and tRNA